GEO series
NSABP B-41: A Study of AC Followed by a Combination of Paclitaxel Plus Trastuzumab or Lapatinib or Both Given Before Surgery to Patients With Operable HER2 Positive Invasive Breast Cancer [B41_27_POST]
GSE275065
Homo sapiens (human)
RNA-seq (gene expression)
27 samples
Submitted 2025/08/13
Platform GPL24676
At a glance
RNA-seq (gene expression) · human · 27 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Homo sapiens (human)
- Topic
- Breast cancerThis series is part of our curated briefing on it.
- Samples
- 27 samples: 27 samples, each with a distinct title — no replicated groupsGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- Prognostic value of residual disease (RD) biology and gene expression changes during the neoadjuvant treatment in patients with HER2-positive early breast cancer (EBC)Annals of oncology : official journal of the European Society for Medical Oncology · 2025
Summary (written by the submitters)
Background: We studied the effect on tumour response to neoadjuvant therapy of the substitution of lapatinib for trastuzumab in combination with weekly paclitaxel after doxorubicin plus cyclophosphamide treatment, and of the addition of lapatinib and trastuzumab combined after doxorubicin plus cyclophosphamide treatment in patients with HER2-positive operable breast cancer to determine whether there would be a benefit of dual HER2 blockade in these patients.
Read the full summary ↓
Methods: For this open-label, randomised phase 3 trial we recruited women aged 18 years or older with an ECOG performance status of 0 or 1 with operable HER2-positive breast cancer. Each received four cycles of standard doxorubicin 60 mg/m(2) and cyclophosphamide 600 mg/m(2) intravenously on day 1 every 3 weeks followed by four cycles of weekly paclitaxel (80 mg/m(2)) intravenously on days 1, 8, and 15, every 4 weeks. Concurrently with weekly paclitaxel, patients received either trastuzumab (4 mg/kg load, then 2 mg/kg intravenously) weekly until surgery, lapatinib (1250 mg orally) daily until surgery, or weekly trastuzumab plus lapatinib (750 mg orally) daily until surgery. After surgery, all patients received trastuzumab to complete 52 weeks of HER2-targeted therapy. Randomisation (ratio 1:1:1) was done centrally with stratification by clinical tumour size, clinical nodal status, hormone-receptor status, and age. The primary endpoint was the pathological complete response in the breast, and analysis was performed on an intention-to-treat population. Findings: Patient accrual started on July 16, 2007, and was completed on June 30, 2011; 529 women were enrolled in the trial. 519 patients had their pathological response determined. Breast pathological complete response was noted in 93 (52·5%, 95% CI 44·9-59·5) of 177 patients in the trastuzumab group, 91 (53·2%, 45·4-60·3) of 171 patients in the lapatinib group (p=0·9852); and 106 (62·0%, 54·3-68·8) of 171 patients in the combination group (p=0·095). The most common grade 3 and 4 toxic effects were neutropenia (29 [16%] patients in the trastuzumab group [grade 4 in five patients (3%), 28 [16%] in the lapatinib group [grade 4 in eight patients (5%)], and 29 [17%] in the combination group [grade 4 in nine patients (5%)]) and grade 3 diarrhoea (four [2%] patients in the trastuzumab group, 35 [20%] in the lapatinib group, and 46 [27%] in the combination group; p<0·0001). Symptomatic congestive heart failure defined as New York Heart Association Class III or IV events occurred in seven (4%) patients in the trastuzumab group, seven (4%) in the lapatinib group, and one (<1%) in the combination group; p=0·185). Interpretation: Substitution of lapatinib for trastuzumab in combination with chemotherapy resulted in similar high percentages of pathological complete response. Combined HER2-targeted therapy produced a numerically but insignificantly higher pathological complete response percentage than single-agent HER2-directed therapy; these findings are consistent with results from other studies. Trials are being undertaken to further assess these findings in the adjuvant setting. Trial registration: ClinicalTrials.gov NCT00486668.
Published in
Fernandez-Martinez A, Tanioka M, Ahn SG et al.
· Annals of oncology : official journal of the European Society for Medical Oncology 2025
· PMID 39706338
· doi:10.1016/j.annonc.2024.12.010
This dataset
Download · which file do I need?
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
1 · Just have a look
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
2 · Re-analyse it
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE275065_RAW.tar (it can run to tens of gigabytes).
3 · Start from the raw reads
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1149043. Searching any of these in the dataset finder brings you back here.
Study design
27 samples, each with a distinct title — no replicated groups
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 27 sample titles: 27 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
Samples in this study
- GSM8464841 Primary breast tumor, RNAseq, B41_23_E9_T_S96
- GSM8464842 Primary breast tumor, RNAseq, B41_24_3B_T_S51
- GSM8464843 Primary breast tumor, RNAseq, B41_30_15_T_S52
- GSM8464844 Primary breast tumor, RNAseq, B41_79_A3_T_S41
- GSM8464845 Primary breast tumor, RNAseq, B41_84_A4_T_S63
- GSM8464846 Primary breast tumor, RNAseq, B41_105_1A_T_S87
- GSM8464847 Primary breast tumor, RNAseq, B41_130_M_T_S75
- GSM8464848 Primary breast tumor, RNAseq, B41_147_2H_T_S43
- GSM8464849 Primary breast tumor, RNAseq, B41_164_2_T_S96
- GSM8464850 Primary breast tumor, RNAseq, B41_177_A1_T_S6
- GSM8464851 Primary breast tumor, RNAseq, B41_178_J15_T_S8
- GSM8464852 Primary breast tumor, RNAseq, B41_214_C5_T_S32
- GSM8464853 Primary breast tumor, RNAseq, B41_226_B9_T_S34
- GSM8464854 Primary breast tumor, RNAseq, B41_236_A4_T_S90
- GSM8464855 Primary breast tumor, RNAseq, B41_288_D5_T_S25
- GSM8464856 Primary breast tumor, RNAseq, B41_346_A5_T_S48
- GSM8464857 Primary breast tumor, RNAseq, B41_312_A5_T_S30
- GSM8464858 Primary breast tumor, RNAseq, B41_305_1A_T_S27
- GSM8464859 Primary breast tumor, RNAseq, B41_313_C13_T_S32
- GSM8464860 Primary breast tumor, RNAseq, B41_321_1D_T_S40
- GSM8464861 Primary breast tumor, RNAseq, B41_329_A14_T_S35
- GSM8464862 Primary breast tumor, RNAseq, B41_512_A4_T_S85
- GSM8464863 Primary breast tumor, RNAseq, B41_363_1H_T_S47
- GSM8464864 Primary breast tumor, RNAseq, B41_401_B8_T_S75
- GSM8464865 Primary breast tumor, RNAseq, B41_416_3_T_S76
- GSM8464866 Primary breast tumor, RNAseq, B41_493_C40_T_S82
- GSM8464867 Primary breast tumor, RNAseq, B41_506_B2_T_S84
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Share this dataset
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.